Londo did not order the attack on Narn. When Refa told Londo about what he was going to do, Londo was horrified. But he went along with it. And after that, he decided they had already reached the point of no return, so that when the inevitable post-mass-driver occupation atrocities were occuring, he knew about them and did his part, beaurocratically, to make them happen. He explains this to Vir when he rubbed it all in the face of that new Narn envoy who was sent to B5 for one episode (a favorite scene of mine).

The theme of remaining silent is repeated when Cartagia rips out G'Kar's eye, but that time in a more abstract and personal way.

Londo had him killed because Morden told him that Refa killed her, when of course it was Morden who did it in order to get Londo working for the Shadows again. Londo told the Narn that he was reponsible for the horrors against them so that they'd have a personal (and therefore much more violent) stake in assassinating Refa, and that part was true.